Contacts of the strand formed by residues 244 - 249 (chain Q) in PDB entry 2WQT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 244 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179P LYS* 3.7 11.9 - - - +
91Q ASN* 3.4 30.3 + - - +
186Q THR* 3.8 1.2 + - - +
187Q ARG* 3.5 1.4 - - - -
188Q ASN* 2.8 48.3 + - - +
189Q ASN* 4.7 9.7 + - - +
242Q GLY 4.8 0.9 - - - +
243Q ASP* 1.3 74.2 - - - +
245Q PHE* 1.3 64.3 + - - +
246Q GLU* 2.8 38.9 + - - +
256Q ALA* 3.9 10.4 - - - +
257Q ALA 3.5 5.2 - - - +
258Q THR* 3.6 24.5 + - + +
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Residues in contact with PHE 245 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q ILE* 3.0 46.7 - - + -
137Q LEU* 4.6 13.2 - - + -
185Q MET* 4.2 11.2 - - - -
186Q THR 3.3 15.7 - - - -
187Q ARG* 3.6 30.5 - - + -
192Q VAL* 4.2 1.8 - - + -
237Q VAL* 3.5 12.1 - - + -
238Q ALA 3.8 12.8 - - - -
239Q VAL* 3.9 12.3 - - + -
243Q ASP* 3.5 22.2 - - + -
244Q ARG* 1.3 77.6 - - - +
246Q GLU* 1.3 61.8 + - - +
256Q ALA* 3.1 5.2 - - - +
257Q ALA* 2.8 39.9 + - + +
259Q PHE* 3.9 14.6 - + + -
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Residues in contact with GLU 246 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179P LYS* 3.1 19.7 + - - -
180P ASN* 5.0 2.1 - - - +
137Q LEU* 5.2 0.4 - - - -
184Q LYS 3.9 0.9 - - - +
185Q MET* 3.3 2.7 - - - -
186Q THR* 2.8 48.5 + - - +
189Q ASN* 5.7 0.9 - - - +
244Q ARG* 2.8 34.6 + - - +
245Q PHE* 1.3 76.0 - - - +
247Q ALA* 1.3 63.3 + - - +
248Q HIS* 3.6 31.9 + - + +
254Q SER* 3.9 12.8 + - - -
255Q VAL 3.2 9.2 - - - +
256Q ALA* 4.3 2.4 - - + +
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Residues in contact with ALA 247 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q ALA* 3.8 21.8 - - + -
137Q LEU* 3.8 24.4 - - + +
183Q MET* 4.8 2.0 - - + -
184Q LYS 3.4 7.0 - - - +
185Q MET* 4.1 7.4 - - + -
246Q GLU* 1.3 74.6 - - - +
248Q HIS* 1.3 62.6 + - - +
249Q ILE* 5.3 1.8 - - + -
254Q SER* 3.1 8.7 - - - -
255Q VAL* 2.8 38.0 + - + +
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Residues in contact with HIS 248 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Q ALA 3.5 1.6 - - - +
183Q MET* 3.2 7.3 - - - +
184Q LYS* 2.8 44.6 + - + +
186Q THR* 5.9 4.3 - - + -
246Q GLU* 3.6 34.6 - - + +
247Q ALA* 1.3 79.7 - - - +
249Q ILE* 1.3 61.0 + - - +
250Q GLU 4.0 0.7 - - - +
253Q GLY 3.7 3.8 + - - +
254Q SER* 3.9 12.8 - - - -
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Residues in contact with ILE 249 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q ALA* 4.7 5.4 - - + -
107Q GLU 3.6 26.9 - - - +
108Q ILE* 4.5 3.1 - - + -
135Q PRO* 3.8 22.9 - - + -
136Q ALA 4.5 2.2 - - - +
181Q CYS* 3.9 20.0 - - + +
182Q ALA 3.4 1.8 - - - -
183Q MET* 4.0 8.3 - - + -
233Q LEU* 3.8 24.9 - - + -
247Q ALA* 5.3 0.9 - - + -
248Q HIS* 1.3 77.3 - - - +
250Q GLU* 1.3 65.5 + - - +
251Q GLY 3.3 0.7 + - - -
252Q ILE* 3.0 32.3 + - + -
253Q GLY 2.8 35.9 + - - +
255Q VAL* 4.9 4.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il